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Items: 1 to 50 of 79

1.

SKESA: strategic k-mer extension for scrupulous assemblies.

Souvorov A, Agarwala R, Lipman DJ.

Genome Biol. 2018 Oct 4;19(1):153. doi: 10.1186/s13059-018-1540-z.

2.

How user intelligence is improving PubMed.

Fiorini N, Leaman R, Lipman DJ, Lu Z.

Nat Biotechnol. 2018 Oct 1. doi: 10.1038/nbt.4267. [Epub ahead of print]

PMID:
30272675
3.

Towards PubMed 2.0.

Fiorini N, Lipman DJ, Lu Z.

Elife. 2017 Oct 30;6. pii: e28801. doi: 10.7554/eLife.28801.

4.

GenBank.

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2017 Jan 4;45(D1):D37-D42. doi: 10.1093/nar/gkw1070. Epub 2016 Nov 28.

5.

GenBank.

Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72. doi: 10.1093/nar/gkv1276. Epub 2015 Nov 20.

6.

GenBank.

Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2015 Jan;43(Database issue):D30-5. doi: 10.1093/nar/gku1216. Epub 2014 Nov 20.

7.

GenBank.

Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D32-7. doi: 10.1093/nar/gkt1030. Epub 2013 Nov 11.

8.

Biology Direct: celebrating 7 years of open, published peer review.

Koonin EV, Landweber LF, Lipman DJ.

Biol Direct. 2013 Apr 30;8:11. doi: 10.1186/1745-6150-8-11. No abstract available.

9.

Why does a protein's evolutionary rate vary over time?

Du X, Lipman DJ, Cherry JL.

Genome Biol Evol. 2013;5(3):494-503. doi: 10.1093/gbe/evt024.

10.

NIH funding: Agency rebuts critique.

Santangelo G, Lipman DJ.

Nature. 2013 Jan 3;493(7430):26. doi: 10.1038/493026a. No abstract available.

PMID:
23282354
11.

GenBank.

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. doi: 10.1093/nar/gks1195. Epub 2012 Nov 27.

12.

Sequential seasonal H1N1 influenza virus infections protect ferrets against novel 2009 H1N1 influenza virus.

Carter DM, Bloom CE, Nascimento EJ, Marques ET, Craigo JK, Cherry JL, Lipman DJ, Ross TM.

J Virol. 2013 Feb;87(3):1400-10. doi: 10.1128/JVI.02257-12. Epub 2012 Oct 31.

13.

Complex patterns of human antisera reactivity to novel 2009 H1N1 and historical H1N1 influenza strains.

Carter DM, Lu HR, Bloom CE, Crevar CJ, Cherry JL, Lipman DJ, Ross TM.

PLoS One. 2012;7(7):e39435. doi: 10.1371/journal.pone.0039435. Epub 2012 Jul 17.

14.

Domain enhanced lookup time accelerated BLAST.

Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL.

Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12.

15.

GenBank.

Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2012 Jan;40(Database issue):D48-53. doi: 10.1093/nar/gkr1202. Epub 2011 Dec 5.

16.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25. doi: 10.1093/nar/gkr1184. Epub 2011 Dec 2.

17.

Projection of seasonal influenza severity from sequence and serological data.

Wolf YI, Nikolskaya A, Cherry JL, Viboud C, Koonin E, Lipman DJ.

PLoS Curr. 2010 Dec 3;2:RRN1200. doi: 10.1371/currents.RRN1200.

18.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51. doi: 10.1093/nar/gkq1172. Epub 2010 Nov 21.

19.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7. doi: 10.1093/nar/gkq1079. Epub 2010 Nov 10.

20.

Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes.

Wolf YI, Gopich IV, Lipman DJ, Koonin EV.

Genome Biol Evol. 2010 Jul 12;2:190-9. doi: 10.1093/gbe/evq010.

21.

Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.

Cherry JL, Lipman DJ, Nikolskaya A, Wolf YI.

PLoS Curr. 2009 Aug 18;1:RRN1001.

22.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2010 Jan;38(Database issue):D46-51. doi: 10.1093/nar/gkp1024. Epub 2009 Nov 12.

23.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12.

24.

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.

Huang Y, Koonin EV, Lipman DJ, Przytycka TM.

Nucleic Acids Res. 2009 Nov;37(20):6799-810. doi: 10.1093/nar/gkp712. Epub 2009 Sep 10.

25.

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.

Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ.

Proc Natl Acad Sci U S A. 2009 May 5;106(18):7273-80. doi: 10.1073/pnas.0901808106. Epub 2009 Apr 7.

26.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. doi: 10.1093/nar/gkn723. Epub 2008 Oct 21.

27.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J.

Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. doi: 10.1093/nar/gkn741. Epub 2008 Oct 21. Erratum in: Nucleic Acids Res. 2009 May;37(9):3124.

28.

Differences in evolutionary pressure acting within highly conserved ortholog groups.

Przytycka TM, Jothi R, Aravind L, Lipman DJ.

BMC Evol Biol. 2008 Jul 17;8:208. doi: 10.1186/1471-2148-8-208.

29.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2008 Jan;36(Database issue):D25-30. Epub 2007 Dec 11.

30.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. Epub 2007 Nov 27.

31.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2007 Jan;35(Database issue):D21-5.

32.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12. Epub 2006 Dec 14.

33.

Stochastic processes are key determinants of short-term evolution in influenza a virus.

Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC.

PLoS Pathog. 2006 Dec;2(12):e125. Erratum in: PLoS Pathog. 2006 Dec;2(12):e138. Ghedi, Elodie [corrected to Ghedin, Elodie].

34.
35.

Comment on "Large-scale sequence analysis of avian influenza isolates".

Holmes EC, Lipman DJ, Zamarin D, Yewdell JW.

Science. 2006 Sep 15;313(5793):1573; author reply 1573.

36.

A community experiment with fully open and published peer review.

Koonin EV, Landweber LF, Lipman DJ.

Biol Direct. 2006 Jan 31;1:1. No abstract available.

37.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D173-80.

38.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D16-20.

39.

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL.

Nature. 2005 Oct 20;437(7062):1162-6. Epub 2005 Oct 5.

PMID:
16208317
40.

Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.

Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK.

PLoS Biol. 2005 Sep;3(9):e300. Epub 2005 Jul 26.

41.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D39-45.

42.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D34-8.

43.

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.

Shabalina SA, Ogurtsov AY, Rogozin IB, Koonin EV, Lipman DJ.

Nucleic Acids Res. 2004 Mar 18;32(5):1774-82. Print 2004.

44.

GenBank: update.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.

45.

Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.

Shabalina SA, Ogurtsov AY, Lipman DJ, Kondrashov AS.

Nucleic Acids Res. 2003 Sep 15;31(18):5433-9.

46.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.

Nucleic Acids Res. 2003 Jan 1;31(1):23-7.

47.

The relationship of protein conservation and sequence length.

Lipman DJ, Souvorov A, Koonin EV, Panchenko AR, Tatusova TA.

BMC Evol Biol. 2002 Nov 1;2:20. Epub 2002 Nov 1.

48.

CDART: protein homology by domain architecture.

Geer LY, Domrachev M, Lipman DJ, Bryant SH.

Genome Res. 2002 Oct;12(10):1619-23.

49.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL.

Nucleic Acids Res. 2002 Jan 1;30(1):17-20.

50.

Lineage-specific loss and divergence of functionally linked genes in eukaryotes.

Aravind L, Watanabe H, Lipman DJ, Koonin EV.

Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11319-24.

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